Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Gabor Grothendieck
Just a few other points: - vignettes are potentially of interest even before you download the package in order to decide whether the package is of interest. The discussion so far here does not address that. If I am interested in mypackage I will typically google for CRAN mypackage and then loo

Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Seth Falcon
Simon Urbanek <[EMAIL PROTECTED]> writes: > On May 15, 2007, at 1:57 PM, Prof Brian Ripley wrote: > >> On Mon, 14 May 2007, Seth Falcon wrote: >> >>> Duncan Murdoch <[EMAIL PROTECTED]> writes: I'm interested in making vignettes more visible. Putting them on the menu is not the only

Re: [Rd] Unexpected alteration of data frame column names

2007-05-15 Thread Marc Schwartz
On Mon, 2007-05-14 at 23:59 -0700, Herve Pages wrote: > Hi, > > I'm using data.frame(..., check.names=FALSE), because I want to create > a data frame with duplicated column names (in the real life you can get such > data frame as the result of an SQL query): > > > df <- data.frame(aa=1:5, aa=9:

Re: [Rd] optim bug (PR#9684)

2007-05-15 Thread Andrew Clausen
On Tue, May 15, 2007 at 07:02:56PM +0100, Prof Brian Ripley wrote: > In R you rarely need to pass additional arguments in programming as > lexical scoping can be used to capture them. You can also use currying, like this: ll <- function(data) function(params) { #

Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Simon Urbanek
On May 15, 2007, at 1:57 PM, Prof Brian Ripley wrote: > On Mon, 14 May 2007, Seth Falcon wrote: > >> Duncan Murdoch <[EMAIL PROTECTED]> writes: >>> I'm interested in making vignettes more visible. Putting them on >>> the >>> menu is not the only way, but since you're offering to do the >>> w

Re: [Rd] optim bug (PR#9684)

2007-05-15 Thread Prof Brian Ripley
There quite a lot of these: optimize, uniroot, nlm for example. I don't think the problem is large enough to merit another argument. It is tempting to move '...' up the argument list so that partial matching will not occur. I am not sure how far you can go: ?optim has positional matching for '

Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Prof Brian Ripley
On Mon, 14 May 2007, Seth Falcon wrote: > Duncan Murdoch <[EMAIL PROTECTED]> writes: >> I'm interested in making vignettes more visible. Putting them on the >> menu is not the only way, but since you're offering to do the work, I >> think it's a good idea :-). > > Excellent :-) > >> A few questio

Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Simon Urbanek
On May 14, 2007, at 7:15 PM, Seth Falcon wrote: > Hello, > > The vignette concept, which started in Bioconductor, seems to be > catching on. They are supported by R CMD build/check and > documented in the Writing R Extensions manual. I think vignettes > are a fantastic way to introduce ne

Re: [Rd] R (PR#9686)

2007-05-15 Thread Simon Urbanek
Please read the R for Mac FAQ (and in fact the posting guide as well!). This is not a bug is R, you a have a broken 3rd-party plugin as the message tells you. Cheers,m Simon On May 15, 2007, at 1:23 AM, [EMAIL PROTECTED] wrote: > Full_Name: Chiadi Onyike > Version: 2.5 > OS: Mac OS 10.4.9 > S

Re: [Rd] optim bug (PR#9684)

2007-05-15 Thread Bill Dunlap
On Tue, 15 May 2007, Prof Brian Ripley wrote: > This is not a bug, but as documented on the help page: > > ...: Further arguments to be passed to 'fn' and 'gr'. Beware of >partial matching to earlier arguments. > > You have partial matching to 'upper'. We have this problem in op

Re: [Rd] Rgui open script file selection filter wish

2007-05-15 Thread Prof Brian Ripley
This should be quite easy to change in src/gnuwin32/editor.c, but are you able to submit a tested patch? Much easier for you to test than people who don't use the in-built editor much. If so, R-windows is the appropriate list. On Tue, 15 May 2007, Jonathan Swinton wrote: > > When using the F

[Rd] Rgui open script file selection filter wish

2007-05-15 Thread Jonathan Swinton
When using the File/Open Script.. dialogue on Windows, the list of filters offered is R files (*.R) S files (*.q,*.ssc,*.S) All files (*.*) I wish that an additional filter be offered as Sweave files (*.Rnw,*.Snw) I find that the Rgui script editor is adequate for most of my R development

Re: [Rd] XML parsing under R / Extracting nodes’ va lues

2007-05-15 Thread Duncan Temple Lang
You can use getNodeSet() as Hin-Tak suggests. But you will need to do it for each of the target nodes. So you can use sapply() to loop over these. However, if these nodes are all children of the same XML node, you can get the values as # This is the document content. z = "2 2 5 2000" # pars

Re: [Rd] getNamespaceExports("base") error

2007-05-15 Thread ml-it-r-devel
Prof Brian Ripley wrote: > It would seem more logical to use x. Today it has the > same contents as baseenv() (but a different enclosing env), but that may > change. > > I do wonder why you are using this: the R code clearly doesn't. For > base is not a normal namespace and is automatically im

[Rd] error in help file for bartlett.test() (PR#9688)

2007-05-15 Thread D . A . Cairns
Hi, =20 I'm not sure if this is appropriate as this is not really a bug but rather an error in a help file, I could find no address to report documentation errors to though. =20 In the help file in R2.4.1 and R2.5.0 on Windows XP pro the reference in bartlett.test() is incorrectly detailed as:

Re: [Rd] read.table() can't read in this table (But Splus can)

2007-05-15 Thread Liaw, Andy
It's the quoting character(s). This following seems to read the file in correctly: R> DF <- read.table("http://llmpp.nih.gov/DLBCL/NEJM_Web_Fig1data";, + header = TRUE, sep = "\t", quote="") R> str(DF) 'data.frame': 7399 obs. of 295 variables: [...] If I have to guess, it's

Re: [Rd] read.table() can't read in this table (But Splus can) (PR#9687)

2007-05-15 Thread marc_schwartz
On Mon, 2007-05-14 at 23:41 +0200, [EMAIL PROTECTED] wrote: > Full_Name: vax, 9000 > Version: 2.4.0, 2.2.1 > OS: 2.4.0: Mac OS X; 2.2.1: Linux > Submission from: (NULL) (192.35.79.70) > > > To reproduce this bug, first go to the website "http://llmpp.nih.gov/DLBCL/"; > and > download the 14.8M d

Re: [Rd] XML parsing under R / Extracting nodes’ v alues

2007-05-15 Thread Hin-Tak Leung
- you should have posted to either R-help or (more appropriately) to the omega-help list. That said, you need something like this: root.node <- xmlTreeParse(x, useInternalNodes = TRUE) nbrelation.set <- getNodeSet(root.node, "//nbRelations") nbrelation.list <- sapply(nbrelation.set, function(x) {

Re: [Rd] getNamespaceExports("base") error

2007-05-15 Thread Prof Brian Ripley
It would seem more logical to use .BaseNamespaceEnv. Today it has the same contents as baseenv() (but a different enclosing env), but that may change. I do wonder why you are using this: the R code clearly doesn't. For base is not a normal namespace and is automatically imported into every ot

[Rd] getNamespaceExports("base") error

2007-05-15 Thread ml-it-r-devel
Hi! >getNamespaceExports("base") Error in ls(NULL, all = TRUE) : using 'as.environment(NULL)' is defunct getNamespaceExports function (ns) { ns <- asNamespace(ns) if (isBaseNamespace(ns)) ls(NULL, all = TRUE) else ls(getNamespaceInfo(ns, "exports"), all = TRUE) } One p

Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Thomas Friedrichsmeier
On Tuesday 15 May 2007, Duncan Murdoch wrote: > I'm interested in making vignettes more visible.  Putting them on the > menu is not the only way, but since you're offering to do the work, I > think it's a good idea :-). [...] > - Should they appear in a top level Vignettes menu, or as a subme

Re: [Rd] RFC: allow packages to advertise vignettes on Windows

2007-05-15 Thread Friedrich Leisch
> On Mon, 14 May 2007 20:58:11 -0400, > Duncan Murdoch (DM) wrote: > [ ... GUI stuff deleted ] I'm of course very much in favor of adding vignettes automatically to the GUI. > By the way, another way to expose vignettes is to have them > automatically added to the package hel

Re: [Rd] Calling erf function in package NORMT3 produce a R crash on Linux/AMD opteron (PR#9683)

2007-05-15 Thread Prof Brian Ripley
This is a known problem, reported to the package maintainer (the use of R-bugs is inappropriate for contributed packages) over two years ago. On Mon, 14 May 2007, [EMAIL PROTECTED] wrote: > Full_Name: Benjamin Leblanc > Version: 2.4.1 and 2.5.0 > OS: Ubuntu Linux 7.04 AMD64 > Submission from: (N

[Rd] Unexpected alteration of data frame column names

2007-05-15 Thread Herve Pages
Hi, I'm using data.frame(..., check.names=FALSE), because I want to create a data frame with duplicated column names (in the real life you can get such data frame as the result of an SQL query): > df <- data.frame(aa=1:5, aa=9:5, check.names=FALSE) > df aa aa 1 1 9 2 2 8 3 3 7